Cluster Identification
2023-01-12
Last updated: 2024-01-17
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| Rmd | bca1a73 | Andreas Chiocchetti | 2024-01-09 | intermediate stage bulk seq |
Clustering Analysis
Clustering after batch correction
Centering and scaling data matrixPC_ 1
Positive: STMN2, NSG2, NEUROD6, INA, NEUROD2, BHLHE22, CXADR, SLA, GAP43, NELL2
TTC9B, GRIA2, MYT1L, LRRC7, MLLT3, LBH, UCHL1, DLX6-AS1, STMN4, OCIAD2
CNR1, SYT4, ENC1, MEF2C, SNAP25, RUNX1T1, ERBB4, SNCB, ZBTB18, GRIA1
Negative: SLC1A3, VIM, HMGB2, ZFP36L1, NUSAP1, TOP2A, DBI, PTN, B2M, MKI67
PTTG1, CLU, CD99, PTPRZ1, CDK1, SPARC, PON2, HOPX, UBE2C, METRN
TTYH1, TPX2, PBK, CENPF, ANXA5, MT2A, BCAN, SOX9, PEA15, HSPB1
PC_ 2
Positive: MKI67, UBE2C, TOP2A, NUSAP1, TPX2, CENPF, KIF2C, DLGAP5, ASPM, BIRC5
KNL1, PIMREG, CDC20, CDCA8, NUF2, PBK, CDK1, SGO1, PTTG1, HMGB2
KIF11, PLK1, CCNA2, CKAP2L, KIFC1, GTSE1, CCNB1, NDC80, CENPE, MAD2L1
Negative: CLU, ATP1B2, PTN, AQP4, HOPX, PON2, TFPI, ANOS1, ATP1A2, TTYH1
SPARC, BCAN, SLC1A3, APOE, PSAT1, VIM, PEA15, FAM107A, PTPRZ1, HES1
TIMP3, IL33, LRRC3B, CSPG5, S1PR1, SLCO1C1, SCD, VCAM1, TNC, IQGAP2
PC_ 3
Positive: NEUROD6, NELL2, NEUROD2, MEF2C, BHLHE22, GAP43, ARPP21, SATB2, SERPINI1, SYT4
ZBTB18, SLA, FAM49A, GPR22, NEFM, CAMK2B, GPR85, SNCB, CSRP2, NSG2
CXADR, LINGO1, SATB2-AS1, PLXNA4, DAB1, OCIAD2, GPRIN3, NRN1, PCLO, FAM162A
Negative: DLX6-AS1, PLS3, SCGN, DLX2, DLX5, DLX1, SOX2-OT, GAD2, CALB2, SP9
PDZRN3, ERBB4, RND3, ID4, SMOC1, C1orf61, NNAT, GAD1, WLS, SOX9
NRIP3, TOX3, ST18, HMGN2, AMBN, NRXN3, CDCA7, DBI, BCAN, PCDH9
PC_ 4
Positive: ADM, VEGFA, DDIT4, BNIP3, IGFBP2, P4HA1, PLOD2, EGLN3, SLC16A3, SLC2A1
FAM162A, ENO1, STC2, AKAP12, PGK1, IGFBP5, GAPDH, PDK1, SLC16A1, TPI1
AK4, CEBPB, PKM, MIR210HG, HERPUD1, SHMT2, EMX2, HK2, BHLHE40, CDKN1A
Negative: NTRK2, AQP4, SPARCL1, APOE, GJA1, CST3, SPON1, MEF2C, PMP2, ANOS1
TFPI, S100B, BCAN, CHL1, STMN2, DCLK1, CSPG5, NKAIN4, BBOX1, VCAM1
LINC01896, AGT, CALM1, SATB2, ANGPT1, RANBP3L, SERPINI1, WLS, NELL2, GFAP
PC_ 5
Positive: ENC1, TMEM158, BHLHE22, NEUROD2, EZR, SLA, CSRP2, MLLT3, CNR1, PHLDA1
NEUROD6, CNTNAP2, LHX2, ADRA2A, NKAIN3, ZBTB18, HES6, EOMES, EPHA3, CLMP
NHLH1, FABP7, RASGRP1, NEUROG2, SFRP1, CHRDL1, HS3ST1, PENK, GAP43, GNG5
Negative: DLX6-AS1, PLS3, SCGN, DLX2, SOX2-OT, DLX1, DLX5, PLOD2, STC2, PDZRN3
GPRIN3, GPR22, CALB2, ADM, DDIT4, CALY, BNIP3, SERPINI1, GAD2, ERBB4
VEGFA, H1F0, FAM162A, SP9, PCDH9, IGFBP5, CNTN1, CELF4, PDK1, P4HA1 Computing nearest neighbor graphComputing SNNModularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 9107
Number of edges: 410519
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.9383
Number of communities: 7
Elapsed time: 1 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 9107
Number of edges: 410519
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.9007
Number of communities: 9
Elapsed time: 1 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 9107
Number of edges: 410519
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8746
Number of communities: 14
Elapsed time: 1 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 9107
Number of edges: 410519
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8516
Number of communities: 14
Elapsed time: 1 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 9107
Number of edges: 410519
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8312
Number of communities: 16
Elapsed time: 1 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 9107
Number of edges: 410519
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8164
Number of communities: 19
Elapsed time: 1 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 9107
Number of edges: 410519
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8028
Number of communities: 20
Elapsed time: 1 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 9107
Number of edges: 410519
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.7900
Number of communities: 21
Elapsed time: 1 seconds
UMAP Clustering after batch correction at different resolutions
Saving 8 x 8 in imageCheck stability of clusters
Saving 16 x 8 in imageModularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 9107
Number of edges: 410519
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8746
Number of communities: 14
Elapsed time: 1 secondsoptimize UMAP
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Saving 12 x 12 in imageWarning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session18:59:32 UMAP embedding parameters a = 0.1496 b = 0.8684
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'spam'
18:59:32 Read 9107 rows and found 40 numeric columns
18:59:32 Using Annoy for neighbor search, n_neighbors = 30
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'spam'
18:59:32 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
18:59:34 Writing NN index file to temp file /tmp/RtmpdGKrw2/file14fe5e18f6fa
18:59:34 Searching Annoy index using 1 thread, search_k = 3000
18:59:37 Annoy recall = 100%
18:59:38 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
18:59:40 Initializing from normalized Laplacian + noise (using RSpectra)
18:59:40 Commencing optimization for 500 epochs, with 415428 positive edges
18:59:54 Optimization finishedfinal UMAP clustering
Saving 7 x 5 in image
Saving 8 x 4 in imageCalculate cell cycle scoring
Warning: The following features are not present in the object: FEN1, MLF1IP,
RAD51, not searching for symbol synonymsWarning: The following features are not present in the object: FAM64A, HN1, not
searching for symbol synonyms
Saving 12 x 6 in imageIdentification of clusters
0mM 5mM
0mM 1.0000000 0.6908695
5mM 0.6908695 1.0000000Using type as id variables
Saving 8 x 8 in image
Feature plots UMAP
Saving 8 x 8 in imageWarning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.
Feature plots PCA
Saving 8 x 8 in imageMarkers identification and visualization
Calculating cluster 0For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
(default method for FindMarkers) please install the presto package
--------------------------------------------
install.packages('devtools')
devtools::install_github('immunogenomics/presto')
--------------------------------------------
After installation of presto, Seurat will automatically use the more
efficient implementation (no further action necessary).
This message will be shown once per sessionCalculating cluster 1Calculating cluster 2Calculating cluster 3Calculating cluster 4Calculating cluster 5Calculating cluster 6Calculating cluster 7Calculating cluster 8Calculating cluster 9Calculating cluster 10Calculating cluster 11Calculating cluster 12Calculating cluster 13Warning in DoHeatmap(seurat_integrated, features = top10$gene, slot =
"scale.data"): The following features were omitted as they were not found in
the scale.data slot for the RNA assay: CYP4F26P, PPARG, IGLV1-51, TRHDE-AS1,
AL133375.1, DCHS2, AC026471.3, CNOT6LP1, AC103810.2, ARMC3, LINC01497,
AC084125.2, AC120036.1, POU4F1, NAMPTP1, AC010320.1, LHX5-AS1, AC091182.1,
NKX2-5, HOXD9, MYOD1, LHX5, ULBP1, AL157400.2, UPK1A-AS1, AC099850.3, FAM72C,
FBLN2, HSPB3, MYO3B, IMPG2, VIPR2, LINC00689, TESK2, AP001972.3, DENND1C,
CRYBG2, MCHR1, RELN, EPS8L2, ASCL2, CABP7, FXYD3, PI16, KCNJ16, GJB2, FIBIN,
MME, OXTR, DMRTA1, AC087632.1, KANK2, CDC45, AC099754.1, AC092112.1, IL12A,
CASP1, FMO1, TMEM244, GPR61, AL139275.1, AC010931.2, AKAIN1, CEMIP, LRTM2,
UNC5A, LAMB3, PTGFR, SVEP1, MYOT, CACNA2D3, PTPRR, RGN, THRB
Saving 8 x 15 in imageVisualizing the expression of marker genes with respect to different cell types
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of boundsUsing Group.1 as id variables
Saving 6 x 9 in imagechr 16p11 genes expression by cluster
url could not be opendedcannot open URL 'https://onedrive.live.com/download?id=1CE096496C465FF3!879&resid=1CE096496C465FF3!879&ithint=file%2cxlsx&authkey=!AEkKHImEdX9UvHA&wdo=2&cid=1ce096496c465ff3': HTTP status was '403 Forbidden'trying local insteadError in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of boundsUsing Group.1 as id variables
Saving 6 x 8 in image16p11 genes PA condition
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of boundsUsing Group.1 as id variablesError in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of boundsUsing Group.1 as id variables
Saving 12 x 8 in imagechr16p11 violin plots
The default behaviour of split.by has changed.
Separate violin plots are now plotted side-by-side.
To restore the old behaviour of a single split violin,
set split.plot = TRUE.
This message will be shown once per session.Warning: The following requested variables were not found: BOLA2, SLX1B,
SULT1A4, SULT1A3, SPN, C16orf54, PRRT2, PAGR1, TLCD3BScale for x is already present.
Adding another scale for x, which will replace the existing scale.
Saving 20 x 10 in imageKynurenine genes expression by cluster
url could not be opendedcannot open URL 'https://onedrive.live.com/download?id=1CE096496C465FF3!878&resid=1CE096496C465FF3!878&ithint=file%2cxlsx&authkey=!AMv00cMy5Pg7LLA&wdo=2&cid=1ce096496c465ff3': HTTP status was '403 Forbidden'trying local insteadError in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of boundsUsing Group.1 as id variables
Saving 6 x 6 in imageKynurenine genes PA condition
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of boundsUsing Group.1 as id variablesError in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of boundsUsing Group.1 as id variables
Saving 10 x 6 in imageKynurenine violin plots
Warning: The following requested variables were not found: TDO2 , IDO1, IDO2,
KYNUScale for x is already present.
Adding another scale for x, which will replace the existing scale.
Saving 20 x 10 in imageGO terms of clusters
Detected custom background input, domain scope is set to 'custom'[1] "result" "meta" Loading required package: kableExtra
Attaching package: 'kableExtra'The following object is masked from 'package:dplyr':
group_rowsLoading required package: compareGroupsLoading required package: pheatmapLoading required package: DESeq2
Attaching package: 'DESeq2'The following object is masked from 'package:CATALYST':
plotCountsThe following object is masked from 'package:scater':
fpkm
Saving 15 x 20 in image
Saving 15 x 20 in image
Saving 15 x 20 in image
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] DESeq2_1.40.2 pheatmap_1.0.12
[3] compareGroups_4.7.2 kableExtra_1.3.4
[5] clustree_0.5.1 ggraph_2.1.0
[7] CATALYST_1.24.0 reshape2_1.4.4
[9] pals_1.8 gprofiler2_0.2.2
[11] viridis_0.6.4 viridisLite_0.4.2
[13] cowplot_1.1.2 randomcoloR_1.1.0.1
[15] RCurl_1.98-1.13 RColorBrewer_1.1-3
[17] data.table_1.14.10 lubridate_1.9.3
[19] forcats_1.0.0 stringr_1.5.1
[21] dplyr_1.1.4 purrr_1.0.2
[23] readr_2.1.4 tidyr_1.3.0
[25] tibble_3.2.1 tidyverse_2.0.0
[27] scater_1.28.0 scuttle_1.10.3
[29] Seurat_5.0.1 SeuratObject_5.0.1
[31] sp_2.1-2 SingleCellExperiment_1.24.0
[33] ggpubr_0.6.0 ggplot2_3.4.4
[35] SingleR_2.2.0 SummarizedExperiment_1.32.0
[37] Biobase_2.62.0 GenomicRanges_1.54.1
[39] GenomeInfoDb_1.38.1 IRanges_2.36.0
[41] S4Vectors_0.40.2 BiocGenerics_0.48.1
[43] MatrixGenerics_1.14.0 matrixStats_1.1.0
[45] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] dichromat_2.0-0.1 nnet_7.3-19
[3] goftest_1.2-3 DT_0.31
[5] TH.data_1.1-2 vctrs_0.6.5
[7] spatstat.random_3.2-2 digest_0.6.33
[9] png_0.1-8 shape_1.4.6
[11] git2r_0.33.0 ggrepel_0.9.4
[13] httpcode_0.3.0 deldir_2.0-2
[15] parallelly_1.36.0 fontLiberation_0.1.0
[17] MASS_7.3-60 httpuv_1.6.13
[19] foreach_1.5.2 withr_2.5.2
[21] ggrastr_1.0.2 xfun_0.41
[23] ellipsis_0.3.2 survival_3.5-7
[25] crul_1.4.0 ggbeeswarm_0.7.2
[27] RProtoBufLib_2.12.1 drc_3.0-1
[29] systemfonts_1.0.5 ragg_1.2.7
[31] zoo_1.8-12 GlobalOptions_0.1.2
[33] gtools_3.9.5 V8_4.4.1
[35] pbapply_1.7-2 promises_1.2.1
[37] httr_1.4.7 rstatix_0.7.2
[39] globals_0.16.2 fitdistrplus_1.1-11
[41] ps_1.7.5 rstudioapi_0.15.0
[43] pan_1.9 miniUI_0.1.1.1
[45] generics_0.1.3 processx_3.8.3
[47] curl_5.2.0 zlibbioc_1.48.0
[49] ScaledMatrix_1.8.1 polyclip_1.10-6
[51] GenomeInfoDbData_1.2.11 SparseArray_1.2.2
[53] xtable_1.8-4 doParallel_1.0.17
[55] evaluate_0.23 S4Arrays_1.2.0
[57] glmnet_4.1-8 hms_1.1.3
[59] irlba_2.3.5.1 colorspace_2.1-0
[61] ROCR_1.0-11 reticulate_1.34.0
[63] spatstat.data_3.0-3 magrittr_2.0.3
[65] lmtest_0.9-40 later_1.3.2
[67] lattice_0.22-5 mapproj_1.2.11
[69] spatstat.geom_3.2-7 future.apply_1.11.1
[71] getPass_0.2-4 scattermore_1.2
[73] XML_3.99-0.16 RcppAnnoy_0.0.21
[75] pillar_1.9.0 nlme_3.1-164
[77] iterators_1.0.14 compiler_4.3.1
[79] beachmat_2.16.0 RSpectra_0.16-1
[81] stringi_1.8.3 jomo_2.7-6
[83] minqa_1.2.6 tensor_1.5
[85] plyr_1.8.9 crayon_1.5.2
[87] abind_1.4-5 truncnorm_1.0-9
[89] chron_2.3-61 locfit_1.5-9.8
[91] graphlayouts_1.0.2 sandwich_3.1-0
[93] whisker_0.4.1 codetools_0.2-19
[95] multcomp_1.4-25 textshaping_0.3.7
[97] BiocSingular_1.16.0 openssl_2.1.1
[99] flextable_0.9.4 crosstalk_1.2.1
[101] bslib_0.6.1 GetoptLong_1.0.5
[103] plotly_4.10.3 mime_0.12
[105] splines_4.3.1 circlize_0.4.15
[107] Rcpp_1.0.11 fastDummies_1.7.3
[109] sparseMatrixStats_1.12.2 knitr_1.45
[111] utf8_1.2.4 clue_0.3-65
[113] lme4_1.1-35.1 fs_1.6.3
[115] listenv_0.9.0 checkmate_2.3.1
[117] nnls_1.5 DelayedMatrixStats_1.22.6
[119] openxlsx_4.2.5.2 ggsignif_0.6.4
[121] Matrix_1.6-4 callr_3.7.3
[123] tzdb_0.4.0 svglite_2.1.3
[125] tweenr_2.0.2 pkgconfig_2.0.3
[127] tools_4.3.1 cachem_1.0.8
[129] rvest_1.0.3 fastmap_1.1.1
[131] rmarkdown_2.25 scales_1.3.0
[133] grid_4.3.1 ica_1.0-3
[135] officer_0.6.3 broom_1.0.5
[137] sass_0.4.8 patchwork_1.2.0
[139] dotCall64_1.1-1 carData_3.0-5
[141] rpart_4.1.23 RANN_2.6.1
[143] farver_2.1.1 tidygraph_1.3.0
[145] yaml_2.3.8 cli_3.6.2
[147] writexl_1.4.2 webshot_0.5.5
[149] leiden_0.4.3.1 lifecycle_1.0.4
[151] askpass_1.2.0 uwot_0.1.16
[153] mvtnorm_1.2-4 backports_1.4.1
[155] BiocParallel_1.34.2 cytolib_2.12.1
[157] timechange_0.2.0 gtable_0.3.4
[159] rjson_0.2.21 ggridges_0.5.5
[161] progressr_0.14.0 parallel_4.3.1
[163] limma_3.56.2 jsonlite_1.8.8
[165] mitml_0.4-5 RcppHNSW_0.5.0
[167] bitops_1.0-7 openxlsx2_1.2
[169] Rtsne_0.17 FlowSOM_2.8.0
[171] spatstat.utils_3.0-4 BiocNeighbors_1.18.0
[173] zip_2.3.0 flowCore_2.12.2
[175] mice_3.16.0 jquerylib_0.1.4
[177] highr_0.10 lazyeval_0.2.2
[179] shiny_1.8.0 ConsensusClusterPlus_1.64.0
[181] htmltools_0.5.7 sctransform_0.4.1
[183] gfonts_0.2.0 glue_1.6.2
[185] spam_2.10-0 XVector_0.42.0
[187] gdtools_0.3.5 rprojroot_2.0.4
[189] Rsolnp_1.16 gridExtra_2.3
[191] boot_1.3-28.1 igraph_1.6.0
[193] R6_2.5.1 labeling_0.4.3
[195] cluster_2.1.6 nloptr_2.0.3
[197] DelayedArray_0.28.0 tidyselect_1.2.0
[199] vipor_0.4.7 plotrix_3.8-4
[201] maps_3.4.2 xml2_1.3.6
[203] ggforce_0.4.1 fontBitstreamVera_0.1.1
[205] car_3.1-2 future_1.33.1
[207] rsvd_1.0.5 munsell_0.5.0
[209] KernSmooth_2.23-22 fontquiver_0.2.1
[211] htmlwidgets_1.6.4 ComplexHeatmap_2.16.0
[213] rlang_1.1.2 spatstat.sparse_3.0-3
[215] spatstat.explore_3.2-5 uuid_1.1-1
[217] colorRamps_2.3.1 HardyWeinberg_1.7.5
[219] ggnewscale_0.4.9 fansi_1.0.6
[221] beeswarm_0.4.0